trunk/proteinstructure/NodeNbh.java

package proteinstructure;

import java.util.TreeMap;
import java.util.Collections;

public class NodeNbh extends TreeMap<Integer,String> {
        

        private static final long serialVersionUID = 1L;
        
        public static final String centralLetter="x";

        // central residue
        public int central_resser;
        public String central_resType;
        
        public NodeNbh(int i_resser, String i_resType){
                super();
                this.central_resser=i_resser;
                this.central_resType=i_resType;
        }
        
        public String getMotif(){
                String motif="";
                int min=Math.min(central_resser, Collections.min(this.keySet()));
                int max=Math.max(central_resser, Collections.max(this.keySet()));
                for (int i=min;i<=max;i++){
                        if (this.containsKey(i)){
                                motif+=AA.threeletter2oneletter(this.get(i));
                        } else if (i==central_resser){
                                motif+=centralLetter;
                        } else {
                                motif+="_";
                        }
                }
                return motif;
        }

        public String getMotifwg(){
                String motif="";
                int min=Math.min(central_resser, Collections.min(this.keySet()));
                int max=Math.max(central_resser, Collections.max(this.keySet()));
                int gapSize=0;
                String gap="";
                for (int i=min;i<=max;i++){
                        if (this.containsKey(i)){
                                motif+=gap;
                                motif+=AA.threeletter2oneletter(this.get(i));
                                gapSize=0;
                                gap="";
                        } else if (i==central_resser){
                                motif+=gap;
                                motif+=centralLetter;
                                gapSize=0;
                                gap="";
                        } else {
                                gapSize++;
                                gap="_{"+gapSize+"}";
                        }
                }
                return motif;
        }

}
Revision:	179
Committed:	Thu May 31 09:41:41 2007 UTC (17 years, 4 months ago) by duarte
File size:	1420 byte(s)
Log Message:	FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh New method getResidueType
Line	User	Rev	File contents
1	duarte	179	package proteinstructure;
2
3			import java.util.TreeMap;
4			import java.util.Collections;
5
6			public class NodeNbh extends TreeMap<Integer,String> {
7
8
9			private static final long serialVersionUID = 1L;
10
11			public static final String centralLetter="x";
12
13			// central residue
14			public int central_resser;
15			public String central_resType;
16
17			public NodeNbh(int i_resser, String i_resType){
18			super();
19			this.central_resser=i_resser;
20			this.central_resType=i_resType;
21			}
22
23			public String getMotif(){
24			String motif="";
25			int min=Math.min(central_resser, Collections.min(this.keySet()));
26			int max=Math.max(central_resser, Collections.max(this.keySet()));
27			for (int i=min;i<=max;i++){
28			if (this.containsKey(i)){
29			motif+=AA.threeletter2oneletter(this.get(i));
30			} else if (i==central_resser){
31			motif+=centralLetter;
32			} else {
33			motif+="_";
34			}
35			}
36			return motif;
37			}
38
39			public String getMotifwg(){
40			String motif="";
41			int min=Math.min(central_resser, Collections.min(this.keySet()));
42			int max=Math.max(central_resser, Collections.max(this.keySet()));
43			int gapSize=0;
44			String gap="";
45			for (int i=min;i<=max;i++){
46			if (this.containsKey(i)){
47			motif+=gap;
48			motif+=AA.threeletter2oneletter(this.get(i));
49			gapSize=0;
50			gap="";
51			} else if (i==central_resser){
52			motif+=gap;
53			motif+=centralLetter;
54			gapSize=0;
55			gap="";
56			} else {
57			gapSize++;
58			gap="_{"+gapSize+"}";
59			}
60			}
61			return motif;
62			}
63
64			}